The Yacoraite Formation (Cretaceous–Paleogene) is a mixed carbonate–siliciclastic microbialite-bearing lacustrine succession deposited in the intra-continental Salta rift basin (Argentina). In the northern sub-basin of Tres Cruces, the spectacular exposures and high lateral continuity of the outcrops provide a suitable setting to investigate and reconstruct the paleoenvironments of deposition and the resulting facies architecture of this closed, saline lake system. The Yacoraite Formation deposited in a predominantly shallow-water ramp-like lake system, characterized by eighteen main facies, classified within four main facies associations, each defining a particular depositional environment along the lake profile. From proximal (shallow) to distal: i) Palustrine Facies Association; ii) Littoral Facies Association; iii) Sub-littoral Facies Association; and lastly iv) Profundal Facies Association. In the Yacoraite paleo-lake extensive fringing mud-flat environments surrounded the lake margins, while the littoral marginal areas hosted extensive wave-dominated oolitic–bioclastic grainstones forming shoals and bars parallel to the lake margins and provided a sheltered environment in the back-shoals that allowed prolific microbialite development. In proximity to river inputs, shallow-water deltas and shoreline sandstones accumulated in the littoral margins. In the sub-littoral zone, mud-supported carbonates such as ostracod wackestones and mudstones deposited below the fair-weather wave base, and in the profundal settings deep-water organic-rich shales deposited. The Yacoraite paleo-lake evolved from a relatively stable and perennial lake system (lake stage 1) into a rapidly fluctuating ephemeral lake system (stage 2), as a result of progressively changing environmental and climatic conditions toward more arid settings. Climate control is also critical in the facies architecture, with the development of short-term cyclicity, represented by meter-scale transgressive–regressive (T–R) cycles being the result of lacustrine expansion–contraction cycles. The regressive hemicycles represent shallowing-upward succession of sub-littoral and littoral carbonate-dominated facies, whereas the transgressive hemicycles are mostly represented by sub-littoral and profundal mudstones and shales. Stacking of short-term cycles resulted in the development of medium- and long-term cyclicity at the scale of tens of meters, which represent the long-term evolution of the lake system. Lastly, a comparison with two well-documented closed lake systems highlights the role of allogenic factors acting at a regional scale (e.g., climate and tectonics) in controlling the lake-basin type, facies association and the resulting architecture. Factors at the lake-basin scale (e.g., lake margin profile, bathymetry) modulate the expression of facies and cyclicity. Ultimately, the characterization of the kilometer-scale outcrops of the Yacoraite paleo-lake provides a reference analog study to support the characterization of similar depositional systems and reservoirs of other ancient, closed lake systems, including the Pre-Salt Carbonates of the South Atlantic.